MicroBiology

RNA stands for ribonucleic acid. There are different types of RNA like microbial RNA, transfer RNA, ribosomal RNA, small hair pin RNA. In this article let us focus on small hair pin RNA.

A small hairpin RNA (shRNA) is a RNA sequence. It resembles a hair pin and hence the name small hairpin RNA is derived. This sequence of RNA creates a tight hair pin turn, which is used to silence the expressions of genes through the RNA interface. The small hairpin RNA utilizes a vector that is being introduced in a cells and it uses U6 promoter in order to ensure that the small hairpin RNA is expressed always. This vector is generally passed to the daughter cells that allow the inheritation of gene silencing.

The cellular machinery chops the structure of the short hairpin RNA into siRNA. The RISC (RNA induced silencing complex) then brings about the binding of this structure. This complex structure gets bound to the microbial RNAs and cleaves it that matches the siRNA bound to it.

RNA polymerase III brings about the transcription of the short hair pin RNA. The production of short hair pin RNA may sometimes lead to an interferon response in a mammalian cell. This happens because these cells try to defend themselves from what is perceived as viral attack. This does not happen in microbial RNA because the transcription of microbial RNA is carried out by RNA polymerase III.

The small hairpin RNAs are used in plants and other systems, basically those which are not drived by the U6 promoter. In most of the plant species, cauliflower mosaic virus35s promoter is the traditional promoter for a constitutive and strong expression. In such cases RNA polymerase II is utilized for the expression of the transcribed destined in order to initiate RNAi. The other applications of short hair pin RNA consist of developing the cell lines with the loss of function phenotypes.

The structural requirements of short hairpin RNA - 2 different systems were used by Paddison and his Colleagues for accessing the structural requirements of the short pin RNA. In the first system, sea pansy luciferase expression plasmids, firefly luciferase and chemically synthesized short hairpin RNAs were added to the embryo lysapes of Drosophila. The silencing of the short pin RNA is later measured based on the amount of the reduction activity in the firefly luciferase after the sea pansy luciferase levels become normal.

In the second system the similar type of dual luciferase technique was used for measuring the silencing in mamilian cell lines. But, in this approach the short hairpin RNAs were synthesized chemically in vitro transcription or expressed by polymerase III expression plasmids. The small hairpin RNAs are symmetrical bilaterally and their orientation of insertion in polymerase III expression vendor is very significant for their activity.

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